Protein Chemistry Basics

1. Protein ChemistryBasics • Protein function • Protein structure • Primary • Amino acids • Linkage • Protein conformation framework • Dihedral angles • Ramachandran plots • Sequence similarity and variation

2. Protein Function in Cell • Enzymes • Catalyze biological reactions • Structural role • Cell wall • Cell membrane • Cytoplasm

3. Protein Structure

4. Protein Structure

5. Model Molecule: Hemoglobin

6. Hemoglobin: Background • Protein in red blood cells

7. Red Blood Cell (Erythrocyte)

8. Hemoglobin: Background • Protein in red blood cells • Composed of four subunits, each containing a heme group: a ring-like structure with a central iron atom that binds oxygen

9. Heme Groups in Hemoglobin

10. Hemoglobin: Background • Protein in red blood cells • Composed of four subunits, each containing a heme group: a ring-like structure with a central iron atom that binds oxygen • Picks up oxygen in lungs, releases it in peripheral tissues (e.g. muscles)

11. Hemoglobin – Quaternary Structure Two alpha subunits and two beta subunits (141 AA per alpha, 146 AA per beta)

12. Hemoglobin – Tertiary Structure One beta subunit (8 alpha helices)

13. Hemoglobin – Secondary Structure alpha helix

14. β-Hairpin Motif • Simplest protein motif involving two beta strands [from Wikipedia] • adjacent in primary sequence • antiparallel • linked by a short loop • As isolated ribbon or part of betasheet • a special case of a turn • direction of protein backbone reverses • flanking secondary structure elements interact (hydrogen bonds) CS 882 course project

15. Types of Turns • β-turn (most common) • donor and acceptor residues of hydrogen bonds are separated by 3 residues (ii +3 H-bonding) • δ-turn • ii +1 H-bonding • γ-turn • ii +2 H-bonding • α-turn • ii +4 H-bonding • π-turn • ii +5 H-bonding • ω-loop • a longer loop with no internal hydrogen bonding CS 882 course project

16. Structure Stabilizing Interactions • Noncovalent • Van der Waals forces (transient, weak electrical attraction of one atom for another) • Hydrophobic (clustering of nonpolar groups) • Hydrogen bonding

17. Hydrogen Bonding • Involves three atoms: • Donor electronegative atom (D) (Nitrogen or Oxygen in proteins) • Hydrogen bound to donor (H) • Acceptor electronegative atom (A) in close proximity D – H A

18. δ- δ+ δ- D – H A D-H Interaction • Polarization due to electron withdrawal from the hydrogen to D giving D partial negative charge and the H a partial positive charge • Proximity of the Acceptor A causes further charge separation

19. δ- δ+ δ- D – H A D-H Interaction • Polarization due to electron withdrawal from the hydrogen to D giving D partial negative charge and the H a partial positive charge • Proximity of the Acceptor A causes further charge separation • Result: • Closer approach of A to H • Higher interaction energy than a simple van der Waals interaction

20. Hydrogen Bonding And Secondary Structure beta-sheet alpha-helix

21. Structure Stabilizing Interactions • Noncovalent • Van der Waals forces (transient, weak electrical attraction of one atom for another) • Hydrophobic (clustering of nonpolar groups) • Hydrogen bonding • Covalent • Disulfide bonds

22. Disulfide Bonds • Side chain of cysteine contains highly reactive thiol group • Two thiol groups form a disulfide bond

23. Disulfide Bridge

24. Disulfide Bonds • Side chain of cysteine contains highly reactive thiol group • Two thiol groups form a disulfide bond • Contribute to the stability of the folded state by linking distant parts of the polypeptide chain

25. Disulfide Bridge – Linking Distant Amino Acids

26. Hemoglobin – Primary Structure NH2-Val-His-Leu-Thr-Pro-Glu-Glu- Lys-Ser-Ala-Val-Thr-Ala-Leu-Trp- Gly-Lys-Val-Asn-Val-Asp-Glu-Val- Gly-Gly-Glu-….. beta subunit amino acid sequence

27. Protein Structure - Primary • Protein: chain of amino acids joined by peptide bonds

28. Protein Structure - Primary • Protein: chain of amino acids joined by peptide bonds • Amino Acid • Central carbon (Cα) attached to: • Hydrogen (H) • Amino group (-NH2) • Carboxyl group (-COOH) • Side chain (R)

29. General Amino Acid Structure H H2N COOH Cα R

30. General Amino Acid Structure At pH 7.0 H +H3N COO- Cα R

31. General Amino Acid Structure

32. Amino Acids • Chiral

33. Chirality: Glyceraldehyde D-glyderaldehyde L-glyderaldehyde

34. Amino Acids • Chiral • 20 naturally occuring; distinguishing side chain

35. 20 Naturally-occurring Amino Acids

36. Amino Acids • Chiral • 20 naturally occuring; distinguishing side chain • Classification: • Non-polar (hydrophobic) • Charged polar • Uncharged polar

37. Alanine: Nonpolar

38. Serine: Uncharged Polar

39. Aspartic AcidCharged Polar

40. GlycineNonpolar (special case)

41. Peptide Bond • Joins amino acids

42. Peptide Bond Formation

43. Peptide Chain

44. Peptide Bond • Joins amino acids • 40% double bond character • Caused by resonance

46. Peptide bond • Joins amino acids • 40% double bond character • Caused by resonance • Results in shorter bond length

47. Peptide Bond Lengths

48. Peptide bond • Joins amino acids • 40% double bond character • Caused by resonance • Results in shorter bond length • Double bond disallows rotation

49. Protein Conformation Framework • Bond rotation determines protein folding, 3D structure

50. Bond Rotation Determines Protein Folding